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11 results for “ligand docking”
Interformer: An Interaction-Aware Model for Protein-Ligand Docking and Affinity Prediction
<p>The code, dataset, and model weights are described in the paper "Interformer: An Interaction-Aware Model for Protein-Ligand Docking and Affinity Prediction."</p> <p> </p> <p><strong>experiment_results.zip:</strong> Contains generated results that can reproduce the result from the reported paper.</p> <p><strong>benchmark.zip:</strong> Contains docking and affinity input data of the interformer. You can use the source code to make predictions and reproduce the number of the reported paper.</p> <p><strong>checkpoints.zip: </strong>Contains one weight for the Energy and four PoseScore and Affinity models.</p> <p><strong>source_code_1.0.zip:</strong> Contains the initial version of the source code.</p> <p><strong>interformer_train.tar.gz:</strong> Contains prepared training data for interformer. poses/ contains all structure need for training, poses/ligand contains the re-docking poses generated by interformer energy, poses/ligand/rcsb contains the conformation of reference ligand, poses/pocket contains all pocket extract by raw PDB from rcsb, poses/uff contains all ligand conformation minimized using UFF from reference ligand, and train/ contains the training csv.</p> <p><strong>baseline_results.tar.gz:</strong> Contains the predictions from three methods: Interformer, DiffDock, and DeepDock. The results align with the exact numbers reported in the paper. For further details, please refer to the <em>eda/ </em>directory.</p> <p> </p> <p>You can also find the newest version of the source code at <a href="https://github.com/tencent-ailab/Interformer" target="_blank" rel="noopener">https://github.com/tencent-ailab/Interformer</a></p> <p> </p>
AutoDock and CB-Dock data for (NPA)6Zn3(H2O)2 in Synthesis, structural analysis, and docking studies with SARS-CoV-2 of a trinuclear zinc complex with N-phenylanthranilic acid ligands
<p>AutoDock 4.2 and CB-Dock data for (NPA)<sub>6</sub>Zn<sub>3</sub>(H<sub>2</sub>O)<sub>2</sub> with M<sup>pro</sup> from SARS-CoV-2 from PDB Id: 6LU7. </p>
NMR data for (NPA)6Zn3(H2O)2 in Synthesis, structural analysis, and docking studies with SARS-CoV-2 of a trinuclear zinc complex with N-phenylanthranilic acid ligands
<p><sup>1</sup>H, <sup>13</sup>C, COSY, HMBC, and HSQC NMR data in fid format for (NPA)<sub>6</sub>Zn<sub>3</sub>(H<sub>2</sub>O)<sub>2</sub> (NPA = 2-(phenylamino) benzoate) in DMSO-<em>d</em><sub>6.</sub></p>
Data from: Compromise docking power evaluation of liganded crystal structures of Mpro SARS-CoV-2
<p>A set of 406 liganded SARS-CoV-2 M<sup>pro</sup> crystal structures originally downloaded from RCSB PBD database is provided. Ligand and protein files are processed and corrected for various types of structural errors and are provided in pdbqt and mol2 formats for immediate use in molecular docking programs AutoDock, AutoDock Vina, and PLANTS. Data are utilized in calculations of newly defined compromise docking power to monitor the performance of above-mentioned software. The provided dataset can also be used for benchmarking of other software and molecular docking protocols on liganded SARS-CoV-2 M<sup>pro</sup> systems.</p>
Data from: Compromise docking power evaluation of liganded crystal structures of Mpro SARS-CoV-2
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Ligand docking models of vanillic acid decarboxylase (VdcCD)
<p>Docking of substrates and intermediates to the vanillic acid decarboxylase, VdcCD, in models of domain closure.</p>
The impact of the cross-docked poses on the performance of machine learning classifier for protein-ligand binding pose prediction
<p>Datasets, features, and some representative scripts utilized in the paper "The impact of the cross-docked poses on the performance of machine learning classifier for protein-ligand binding pose prediction".</p>
Docking Adenosine Receptor Ligands to SARS-CoV2 mRNA Cap 2'-O-Methyltransferase: Energy Minimized Structures
<p>Energy minimized structures associated with a study docking adenosine receptor binders and related ligands to the adenosine binding site on SARS-CoV2 nsp16. The associated paper is under review, but we have a previous version of the paper available as a preprint at <a href="https://chemrxiv.org/articles/preprint/Docking_Adenosine_Receptor_Ligands_to_SARS-CoV2_mRNA_Cap_Guanine-N7_Methyltransferase/12462080/2">https://chemrxiv.org/articles/preprint/Docking_Adenosine_Receptor_Ligands_to_SARS-CoV2_mRNA_Cap_Guanine-N7_Methyltransferase/12462080/2</a>.</p>
ApoDock: Ligand-Conditioned Sidechain Packing for Flexible Molecular Docking
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A Folding–Docking–Affinity framework for protein–ligand binding affinity prediction
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Dataset for "Identification of Potential inhibitors of the SARS-CoV2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations"
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